Removing internal geometry before 3D printing
All internal faces can be selected by using Select > Internal Faces in the bar on the bottom of the 3D View in Edit Mode.

Since internal faces are Non-manifold geometry, you can also use the shortcut CtrlShiftAltM to select them, along with all other non-manifold geometry.

Once you have the offending faces selected, you can use Del>Faces to remove them without affecting the rest of your geometry.